The economy recession is most likely over, says who?

The economy recession is most likely over, or so says the federal reserve chairman Ben Bernanke. Do you feel it? Are you seeing increased job opportunities when you leave your current lab or security if you have a post-postdoc position? In our industry, where the health of the economy is mostly measured by research budgets of individual labs or research groups, occasionally by budgets for contracting or licensing fees, the change, if any, is still hard-to-find. But hiring at academic institutes like UCSD seems to have picked up lately, probably due to addition grants from the Obama administration’s stimulus programs. At the same time, individual NIH R1 grants have been creeping up to easily around 1 million a year, program grants 3-5 millions. With more stimulus money kicking in to academic labs this fall, it is expected that the situation will further improve. Comments welcome.

Notes about recent jobs in Pharma/Biotech: since our last blog about massive Pfizer layoff of scientists in 02-09-09, a major layoff in the big pharma sector came from Merck, which announced on 06-11-09 that it would cut 16,000 jobs after completing its merger with Shering Plough. On 09-14-09, Eli Lilly reported job cots of 5,500 or roughly 14% of its work force. There are areas in the country where people report about the economy as “I went to 2 grocery stores and 3 discount department stores over one weekend, and you could do cannon shooting practice in there without hitting a person.” Again comments welcome here, if you believe in a turnaround, or it is all doom and gloom to you. Btw, the History channel has been cranking up the 2012 theories for a couple of months now, if you like the doom and gloom theories.

Note added in proof: As reported in Science yesterday, “a new analysis of the grantsmaking process at the National Institutes of Health (NIH) lifts the veil on how many grant proposals are funded even though they fall below a cutoff based on peer-review scores…at least 19% of NIH’s basic research portfolio is funded for reasons that go beyond quality.”

Retroviral Vectors with Integrated oriP/EBNA1 for IPSC

The new product of the week of Sep 21-27 is the retrovirus plasmid sets that contain a built-in episomal expression system. As we have discussed previously, OriP/EBNA1 system originated from Epstein-Bar virus, which allows the establishment of stable episomes at 5-20 copies per cell, and duplication once per cell division.

By using the oriP/EBNA1 episomal system, reprogramming cDNAs can be expressed at prolonged time period in reference to plasmid transfection, without integration into chromosomal DNA. A paper published in PLoS One on Sep 18, 2009 by Marchetto et al. showed that by using such a system (on different plasmids) the authors were able to create induced pluripotent stems cells (iPS cells,) effectively from human embryo neural precursor cells.

The Allele pCHAC-EBNA system has dual functions: it can be ready-to-use plasmids for episomal expression of Oct4, Sox2, c-Myc, Klf4, or Nanog and Lin28 by a simple transfection into target cells; it can also be packaged into retroviruses by transfecting into the Allele Phoenix Retrovirus packaging Eco or Ampho cells. This product group is officially launched today. It should become a highly convenient and unique tool for iPSC-related studies.

Tags: Ampho cells, EBNA, Eco cells, episomal expression, iPS cells, iPSC, iPSCs, New Product of the week, oriP, Phoenix Retroviral System, reprogramming, retroviral vector, retrovirus

HPLC Purified siRNA with Known RNAi Effects at $149/12.5nmol

RNA oligo is significantly more difficult to synthesize than DNA oligos, mainly because the efficiency of coupling each new ribonucleotide during RNA synthesis is a few fold lower than deoxyribonucleotide during DNA synthesis. Typically, there is an ~10% chance a DNA oligo of 21 bases will have a mutation (most frequently a deletion mutation); for an RNA oligo of 21 bases, as in an siRNA pair, such chance is much higher. Furthermore, after combining the sense and antisense siRNA strands, some RNA molecules will remain as single-stranded thereby not fitting for the RNAi apparatus.

RNA interference is a dose-sensitive process — specificity of gene silencing is meaningful only relative to the active concentration of siRNA used. When the concentration is too low, even the most effective siRNAs would fail to cause gene expression knockdown; when too high, non-specific effects will be duly observed. Therefore, it is essential that the concentrations of siRNAs are measured correctly. When doing so, one must consider not only what the apparent concentrations are by OD260 reading, but also whether the RNA strands are of full-length and whether only dsRNA molecules are counted. This issue might not affect data interpretation if appropriate controls are included in one set of RNAi experiments, but it could have significant influence on conclusions if data from different experiment sets or labs are compared or combined.

HPLC purification currently provides the best means to remove RNA molecules with deletions or remain single-stranded, however, the price tag added by most reagent providers for such treatment has been prohibiting because manufacturers either need to start synthesis at a much bigger scale to obtain promised amount, or they do not promise the delivery quantity at all. The phosphoramidites (oligo building blocks) for RNA synthesis can be 10 times or more expensive than for DNA. Some companies offer alternative purification methods such as a cartridge type device, but they can only remove salt and small impurities, not RNA oligos of shorter lengths accumulated at each cycle of amide coupling. The AllHPLC siRNAs within Allele’s RNAi product line, pre-validated or custom made, are uniformly HPLC purified with 5 OD or 12.5 nmol of double-stranded, annealed siRNA delivered. Allele passes to customers the cost savings from manufacturing our own RNA amidites and other reagents for oligo synthesis. The pre-validated HPLC purified double-stranded siRNA is offered today at $149/12.5 nmol.

Before purchasing siRNAs, even at a low cost of $29 per pair of HPLC purified control siRNA from Allele, researchers still need to consider how well their cells can be transfected. For hard-to-transfect cells, lentiviral vectors carrying a shRNA expressing cassette is often a better choice. To establish stable cell lines, plasmid vectors should be considered. For low cost target screening, the PCR format linear siRNA expression cassettes have advantages.

Tags: DNA, gene silencing, HPLC, oligo, reagents for chemical synthesis of DNA and RNA oligonucleotides, reagents for oligonucleotide, RNA, RNA interference, RNAi, shRNA, siRNA

Feeder Cells for Stem Cells

Allele’s entire iPSC product line is designed for the ease of the researcher. Each component in our iPSC catalog will shave priceless time off your protocol by eliminating the tedious steps in iPS induction so you can get down to work.

Allele is adding a major component to its iPSC line: pre-irradiated, ready-to-use, system specific, bFGF-Producing Feeder Cells for iPSC propagation!

Using Allele’s bFGF-Producing Feeder Cells avoids the usual problems associated with MEF cell lines. They are maintained at low passages, come pre-irradiated and ectopically express bFGF so there is no need to supplement your medium with additional growth factors.

Additionally, Allele Biotech is introducing human fibroblasts to the market for iPSC work. MEF is good for mouse iPSC reprogramming but human fibroblast feeders are preferred when creating human iPSCs due to their secreted factors. Propagate human iPSC with greater efficiency while eliminating non-human cells for therapeutic use of human iPSCs!

As always we encourage customer feed back. We are interested to hear about your stem cell work, needs, and requests for new products. We also welcome those who have new ideas and potential products to collaborate with us. We are here to help advance your research and get your technologies to the public.

If you are enjoying AlleleNews and AlleleBlogs: come back and check out our new Forum and FAQ Sections soon to be added to our blogs for quick product/service related exchange and messages of more user control.

Tags: ectopically expressed bFGF, feeder cells, human fibroblast, human iPSC, iPSC induction, optimized iPSC generation, pre-irradiated MEF cells, research help, system specific feeder cells, time efficient iPS generation

Allele Pre-packaged, Titer-determined, Validated iPS Generating Lentivirus Particles

Induced pluripotent stem cell (iPSC) has been an important research area in the past 3 years. These cells have also provided unprecedented possibilities to study cell differentiation and tissue development to biologists in many fields. Allele pre-packaged iPS lentiviral particles are validated, ready-to-use, high quality reagents for any laboratory to create iPS cells. A straight-forward and optimized protocol is also provided for immediate use of these products. iPC cells can be produced typically in 2-3 weeks; but when used in combination with shRNA against p53 (also available from Allele), iPSCs can be produced in just about 5 days!

Follow iPS news on our news page.

Tags: iPS, lentiviral particles, lentivirus, optimized protocol for inducing iPSC, Pre-packaged viral particles, quick iPS induction, titer-determined, validated iPSC